Hi I wanted to do a rma analysis for a affymetrix microarray data. but I got a problem.

Code should be placed in three backticks as shown below

setwd("~/Downloads/GSE24184_RAW/")
library(affy)
library(makecdfenv)
data = ReadAffy()
data

and I got this Error. Please help me to solve this error.


'getOption("repos")' replaces Bioconductor standard repositories, see
'help("repositories", package = "BiocManager")' for details.
Replacement repositories:
    CRAN: https://cran.rstudio.com/
AffyBatch object
size of arrays=476x476 features (22 kb)
cdf=TTHB8401a520105F (??? affyids)
number of samples=14
'getOption("repos")' replaces Bioconductor standard repositories, see
'help("repositories", package = "BiocManager")' for details.
Replacement repositories:
    CRAN: https://cran.rstudio.com/
Error in getCdfInfo(object) : 
  Could not obtain CDF environment, problems encountered:
Specified environment does not contain TTHB8401a520105F
Library - package tthb8401a520105fcdf not installed
Bioconductor - tthb8401a520105fcdf not available
In addition: Warning message:
missing cdf environment! in show(AffyBatch)

Thank you in advance.

> download.file("https://ftp.ncbi.nlm.nih.gov/geo/platforms/GPL9nnn/GPL9209/suppl/GPL9209_TTHB8401a520105F.cdf.gz", "TTHB8401a520105F.cdf.gz")
trying URL 'https://ftp.ncbi.nlm.nih.gov/geo/platforms/GPL9nnn/GPL9209/suppl/GPL9209_TTHB8401a520105F.cdf.gz'
Content type 'application/x-gzip' length 3128959 bytes (3.0 MB)
downloaded 3.0 MB

> make.cdf.package("TTHB8401a520105F.cdf.gz", species = "Bacillis_subtilis", packagename = "tthb8401a520105fcdf" , compress = TRUE)
Reading CDF file.
Creating CDF environment
Wait for about 35 dots...................................
Creating package in C:/Users/jmacdon/Desktop/tthb8401a520105fcdf 



README PLEASE:
A source package has now been produced in
C:/Users/jmacdon/Desktop/tthb8401a520105fcdf.
Before using this package it must be installed via 'R CMD INSTALL'
at a terminal prompt (or DOS command shell).
If you are using Windows, you will need to get set up to install packages.
See the 'R Installation and Administration' manual, specifically
Section 6 'Add-on Packages' as well as 'Appendix E: The Windows Toolset'
for more information.

Alternatively, you could use make.cdf.env(), which will not require you to install a package.
However, this environment will only persist for the current R session
unless you save() it.


> install.packages("tthb8401a520105fcdf", repos = NULL, type = "source")
Installing package into 'C:/Users/jmacdon/AppData/Local/R/win-library/4.2'
(as 'lib' is unspecified)
* installing *source* package 'tthb8401a520105fcdf' ...
** using staged installation
** R
** data
** byte-compile and prepare package for lazy loading
Warning: replacing previous import 'AnnotationDbi::tail' by 'utils::tail' when loading 'tthb8401a520105fcdf'
Warning: replacing previous import 'AnnotationDbi::head' by 'utils::head' when loading 'tthb8401a520105fcdf'
** help
*** installing help indices
** building package indices
** testing if installed package can be loaded from temporary location
Warning: replacing previous import 'AnnotationDbi::tail' by 'utils::tail' when loading 'tthb8401a520105fcdf'
Warning: replacing previous import 'AnnotationDbi::head' by 'utils::head' when loading 'tthb8401a520105fcdf'
** testing if installed package can be loaded from final location
Warning: replacing previous import 'AnnotationDbi::tail' by 'utils::tail' when loading 'tthb8401a520105fcdf'
Warning: replacing previous import 'AnnotationDbi::head' by 'utils::head' when loading 'tthb8401a520105fcdf'
** testing if installed package keeps a record of temporary installation path
* DONE (tthb8401a520105fcdf)
>